Compute Spatial Variables With SpatialAEH Method

spatialAEH()

Compute spatial variable genes with spatialAEH method.

spatialAEH(
    gobject = NULL,
    SpatialDE_results = NULL,
    name_pattern = "AEH_patterns",
    expression_values = c("raw", "normalized", "scaled", "custom"),
    pattern_num = 6,
    l = 1.05,
    python_path = NULL,
    return_gobject = TRUE
)

Arguments

gobject	Giotto object
SpatialDE_results	results of spatialDE() function
name_pattern	name for the computed spatial patterns
expression_values	gene expression values to use
pattern_num	number of spatial patterns to look for
l	lengthscale
python_path	specify specific path to python if required
return_gobject	show plot

Value

An updated Giotto object that incorporates the SpatialDE resutlts.

Details

This function is a wrapper for the automatic expresion histology (AEH) method performed in the SpatialDE function. SpatialDE provides automatic expression histology, a method that groups genes into common spatial patterns (and conversely reveal histological patterns based on gene coexpression).

Note

AEH requires two parameters: the number of patterns, and the characteristic lengthscale for histological patterns.

For more information visit the SpatialDE Github Page.